I think that The Protomen's 2 albums should at least have honorable mention. It's a two-part story based on Capcom's Mega Man series of video games. The first album (self-titled The Protomen) is based directly off of the first few video games and the second (The Father of Death) is a prequel that tells the story of how Dr, Light and Dr. Wiley came to be, how Dr. Wiley used Dr. Light's robotic creations to take over the city. The Protomen were heavily influenced by Styx and, in fact, one of the their band members has the stage name Kilroy.
Also before I even got to #1, I had a feeling 2112 was going to top it off. I think it's the quintessential sci-fi rock opera in the minds of most geeks. I was a bit surprised to see Operation Mindcrime on the list. Although it's a fantastic rock opera and it's one of my favorite albums of all time, I find it to be too gritty and realistic. There's very little sci-fi in Mindcrime as the main character is controlled through drugs and hypnotic suggestion. Mindcrime 2 has a slightly more mystical quality to it since Mary seems to be reaching out to Nikki from beyond the grave. The Warning and Rage for Order are better examples of Queensrche albums with Sci-fi themes. Mindcrime was actually Queensrche's transition album from dark, apocalyptic progressive metal to more realistic cerebral progressive metal as Empire focused more on current issues and psychology.
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